D-amino acids

[pmt706]

D-amino acids are handled less than optimally. We need to address this better.

Should there be a term under MOD:00850, unnatural residue that houses all D-amino acid residues?

Having D amino acid residues related through is_a to their modified L amino acid counterparts doesn't seem quite right.

[javizca]

I would not call them "unnatural residue". They can be found in some organisms in "normal" conditions. Maybe just call the parent term D-amino acids or something like that?

[pmt706]

Good point @javizca. I could hear one of my old professors, Jonathan Sweedler, in my ear even as I typed that. D-amino acids are indeed naturally occurring.

[pabinz]

Actually, they are obtained by racemization of L-residues. They are found in the nature, both as free amino-acids and as residues modified in protein sequences. They can (and must in my opinion) be considered as natural, but not encoded as such. One can consider them as modified L-equivalent residues, as they are not incorporated in this form by the ribosomes into proteins (They are not MOD:00868 in this case).

They are all childs of their L-equivalent (example is D-alanine (Ala)) : MOD:00198.

We can also create a child of MOD:01156 (protein modification categorized by chemical process which can be named racemized residue and put them also there.

I would not create a child of natural residue (MOD:00009), such as natural, D-racemized encoded residue, which becomes a parent of all D-residues. I’m not convinced as this would place each D residues with odd relationships within the MOD:01157 branch.

Therefore:

1) Create a new term named racemized residue as child of MOD:01156

2) Add is_a: MOD:nnnn ! racemized residue for each of the D-residues

3) Add is_a: MOD:mmmm ! modified L-xxxxxx residue for each of the D-residues

Pierre-Alain

De : Paul Thomas @.> Envoyé : mercredi 10 mars 2021 16:42 À : HUPO-PSI/psi-mod-CV @.> Cc : Subscribed @.***> Objet : Re: [HUPO-PSI/psi-mod-CV] D-amino acids (#58)

Good point @javizcahttps://github.com/javizca. I could hear one of my old professors, Jonathan Sweedler, in my ear even as I typed that. D-amino acids are indeed naturally occurringhttps://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b03658.

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